-
1
-
-
0036013593
-
Statistical mechanics of complex networks
-
Albert R., Barabási A.L. Statistical mechanics of complex networks. Rev Mod Phys 2002, 74:47-97.
-
(2002)
Rev Mod Phys
, vol.74
, pp. 47-97
-
-
Albert, R.1
Barabási, A.L.2
-
2
-
-
0025904136
-
Finding maximum cliques in arbitrary and in special graphs
-
Babel L. Finding maximum cliques in arbitrary and in special graphs. Computing 1991, 46:321-341.
-
(1991)
Computing
, vol.46
, pp. 321-341
-
-
Babel, L.1
-
3
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey T.L., Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994, 2:28-36.
-
(1994)
Proc Int Conf Intell Syst Mol Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
4
-
-
0022808049
-
Finding a maximum clique in an arbitrary graph
-
Balas E., Yu C.S. Finding a maximum clique in an arbitrary graph. SIAM J Comput 1986, 15(4):1054-1068.
-
(1986)
SIAM J Comput
, vol.15
, Issue.4
, pp. 1054-1068
-
-
Balas, E.1
Yu, C.S.2
-
5
-
-
0345874725
-
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting
-
Berezikov E., Guryev V., Plasterk R.H.A., Cuppen E. CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. Genome Res 2004, 14:170-178.
-
(2004)
Genome Res
, vol.14
, pp. 170-178
-
-
Berezikov, E.1
Guryev, V.2
Plasterk, R.H.A.3
Cuppen, E.4
-
6
-
-
33746616867
-
Cross-species analysis of biological networks by Bayesian alignment
-
Berg J., Lässig M. Cross-species analysis of biological networks by Bayesian alignment. Proc Natl Acad Sci USA 2006, 103(29):10967-10972.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.29
, pp. 10967-10972
-
-
Berg, J.1
Lässig, M.2
-
8
-
-
0642281348
-
Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
-
Caselle M., Di Cunto F., Provero P. Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes. BMC Bioinformatics 2002, 3:7-16.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 7-16
-
-
Caselle, M.1
Di Cunto, F.2
Provero, P.3
-
9
-
-
0034919548
-
Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis
-
Cliften P.F., Hillier L.W., Fulton L., Graves T., Miner T., Gish W.R., et al. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res 2001, 11:1175-1186.
-
(2001)
Genome Res
, vol.11
, pp. 1175-1186
-
-
Cliften, P.F.1
Hillier, L.W.2
Fulton, L.3
Graves, T.4
Miner, T.5
Gish, W.R.6
-
10
-
-
0038724989
-
Finding functional features in Saccharomyces genomes by phylogenetic footprinting
-
Cliften P., Sudarsanam P., Desikan A., Fulton L., Fulton B., Majors J., et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 2003, 301:71-76.
-
(2003)
Science
, vol.301
, pp. 71-76
-
-
Cliften, P.1
Sudarsanam, P.2
Desikan, A.3
Fulton, L.4
Fulton, B.5
Majors, J.6
-
11
-
-
38549144819
-
A survey of DNA motif finding algorithms
-
Das M., Dai H.K. A survey of DNA motif finding algorithms. BMC Bioinformatics 2007, 8(Suppl.7):S21.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL.7
-
-
Das, M.1
Dai, H.K.2
-
12
-
-
0347492019
-
AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors
-
Davuluri R.V., Sun H., Palaniswamy S.K., Matthews N., Molina C., Kurtz M., et al. AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 2003, 4:25-36.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 25-36
-
-
Davuluri, R.V.1
Sun, H.2
Palaniswamy, S.K.3
Matthews, N.4
Molina, C.5
Kurtz, M.6
-
13
-
-
0018199224
-
DNAse footprinting: a simple method for the detection of protein-DNA binding specificity
-
Galas D.J., Schmitz A. DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 1978, 5(9):3157-3170.
-
(1978)
Nucleic Acids Res
, vol.5
, Issue.9
, pp. 3157-3170
-
-
Galas, D.J.1
Schmitz, A.2
-
14
-
-
33845669975
-
Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea
-
Haberer G., Mader M.T., Kosarev P., Spannagl M., Yang L., Mayer K.F. Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea. Plant Physiol 2006, 142:1589-1602.
-
(2006)
Plant Physiol
, vol.142
, pp. 1589-1602
-
-
Haberer, G.1
Mader, M.T.2
Kosarev, P.3
Spannagl, M.4
Yang, L.5
Mayer, K.F.6
-
15
-
-
0032826179
-
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
-
Hertz G.Z., Stormo G.D. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15:563-577.
-
(1999)
Bioinformatics
, vol.15
, pp. 563-577
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
16
-
-
26444584579
-
Limitations and potentials of current motif discovery algorithms
-
Hu J., Li B., Kihara D. Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res 2005, 33(15):4899-4913.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.15
, pp. 4899-4913
-
-
Hu, J.1
Li, B.2
Kihara, D.3
-
17
-
-
0034628901
-
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
Hughes J.D., Estep P.W., Tavazoie S., Church G.M. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000, 296(5):1205-1214.
-
(2000)
J Mol Biol
, vol.296
, Issue.5
, pp. 1205-1214
-
-
Hughes, J.D.1
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
18
-
-
77951744224
-
Random matrix analysis of localization properties of gene coexpression network
-
Jalan S., Solymosi N., Vattay G., Li B. Random matrix analysis of localization properties of gene coexpression network. Phys Rev E 2010, 81:046118.
-
(2010)
Phys Rev E
, vol.81
, pp. 046118
-
-
Jalan, S.1
Solymosi, N.2
Vattay, G.3
Li, B.4
-
19
-
-
6344241652
-
Conservation and coevolution in the scale-free human gene coexpression network
-
Jordan I.K., Marino-Ramirez L., Wolf Y.I., Koonin E.V. Conservation and coevolution in the scale-free human gene coexpression network. Mol Biol Evol 2004, 21(11):2058-2070.
-
(2004)
Mol Biol Evol
, vol.21
, Issue.11
, pp. 2058-2070
-
-
Jordan, I.K.1
Marino-Ramirez, L.2
Wolf, Y.I.3
Koonin, E.V.4
-
20
-
-
35348992193
-
An improved branch and bound algorithm for the maximum clique problem
-
Konc J., Janežič D. An improved branch and bound algorithm for the maximum clique problem. MATCH Commun Math Comput Chem 2007, 58:569-590.
-
(2007)
MATCH Commun Math Comput Chem
, vol.58
, pp. 569-590
-
-
Konc, J.1
Janežič, D.2
-
21
-
-
0027912333
-
Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment
-
Lawrence C., Altschul S., Boguski M., Liu J., Neuwald A., Wootton J. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 1993, 262:208-214.
-
(1993)
Science
, vol.262
, pp. 208-214
-
-
Lawrence, C.1
Altschul, S.2
Boguski, M.3
Liu, J.4
Neuwald, A.5
Wootton, J.6
-
22
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
-
23
-
-
0035228215
-
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
-
Liu X., Brutlag D.L., Liu J.S. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 2001, 127-138.
-
(2001)
Pac Symp Biocomput
, pp. 127-138
-
-
Liu, X.1
Brutlag, D.L.2
Liu, J.S.3
-
24
-
-
0036324753
-
An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments
-
Liu X.S., Brutlag D.L., Liu J.S. An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments. Nat Biotechnol 2002, 20(8):835-839.
-
(2002)
Nat Biotechnol
, vol.20
, Issue.8
, pp. 835-839
-
-
Liu, X.S.1
Brutlag, D.L.2
Liu, J.S.3
-
25
-
-
34547569191
-
STAMP: a web tool for exploring DNA-binding motif similarities
-
Mahony S., Benos P.V. STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 2007, 35:W253-W258.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Mahony, S.1
Benos, P.V.2
-
26
-
-
71749094192
-
Arabidopsis gene co-expression network and its functional modules
-
Mao L., Hemert J.L.V., Dash S., Dickerson J.A. Arabidopsis gene co-expression network and its functional modules. BMC Bioinformatics 2009, 10:346-369.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 346-369
-
-
Mao, L.1
Hemert, J.L.V.2
Dash, S.3
Dickerson, J.A.4
-
27
-
-
33846061087
-
ATTED-II: a database of co-expressed genes and cis elements for identifying coregulated gene groups in Arabidopsis
-
Obayashi T., Kinoshita K., Nakai K., Shibaoka M., Hayashi S., Saeki M., et al. ATTED-II: a database of co-expressed genes and cis elements for identifying coregulated gene groups in Arabidopsis. Nucleic Acids Res 2007, 35:D863-D869.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Obayashi, T.1
Kinoshita, K.2
Nakai, K.3
Shibaoka, M.4
Hayashi, S.5
Saeki, M.6
-
29
-
-
0038579896
-
The maximum clique problem
-
Pardalos P.M., Xue J. The maximum clique problem. J Global Optim 1994, 4:301-328.
-
(1994)
J Global Optim
, vol.4
, pp. 301-328
-
-
Pardalos, P.M.1
Xue, J.2
-
30
-
-
3242884167
-
Weeder Web: discovery of transcription factor binding sites in a set of sequences from coregulated genes
-
Pavesi G., Mereghetti P., Mauri G., Pesole G. Weeder Web: discovery of transcription factor binding sites in a set of sequences from coregulated genes. Nucleic Acids Res 2004, 32:W199-W203.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Pavesi, G.1
Mereghetti, P.2
Mauri, G.3
Pesole, G.4
-
31
-
-
34247579156
-
A survey of motif discovery methods in an integrated framework
-
Sandve G.K., Drabløs F. A survey of motif discovery methods in an integrated framework. Biol Dir 2006, 1:11-26.
-
(2006)
Biol Dir
, vol.1
, pp. 11-26
-
-
Sandve, G.K.1
Drabløs, F.2
-
32
-
-
13444278955
-
Genomic studies of transcription factor-DNA interactions
-
Sikder D., Kodadek T. Genomic studies of transcription factor-DNA interactions. Curr Opin Chem Biol 2005, 9:38-45.
-
(2005)
Curr Opin Chem Biol
, vol.9
, pp. 38-45
-
-
Sikder, D.1
Kodadek, T.2
-
33
-
-
0042905768
-
YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation
-
Sinha S., Tompa M. YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res 2003, 31:3586-3588.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3586-3588
-
-
Sinha, S.1
Tompa, M.2
-
34
-
-
0345863918
-
AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome
-
Steffens N.O., Galuschka C., Schindler M., Bülow L., Hehl R. AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. Nucleic Acids Res 2004, 32:D368-D372.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Steffens, N.O.1
Galuschka, C.2
Schindler, M.3
Bülow, L.4
Hehl, R.5
-
35
-
-
0034072450
-
DNA binding sites: representation and discovery
-
Stormo G.D. DNA binding sites: representation and discovery. Bioinformatics 2000, 16:16-23.
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
36
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart J.M., Segal E., Koller D., Kim S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302(5643):249-255.
-
(2003)
Science
, vol.302
, Issue.5643
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
37
-
-
0036137323
-
A higher order background model improves the detection of regulatory elements by Gibbs sampling
-
Thijs G., Lescot M., Marchal K., Rombauts S., De Moor B., Rouzé P., et al. A higher order background model improves the detection of regulatory elements by Gibbs sampling. Bioinformatics 2001, 17(12):1113-1122.
-
(2001)
Bioinformatics
, vol.17
, Issue.12
, pp. 1113-1122
-
-
Thijs, G.1
Lescot, M.2
Marchal, K.3
Rombauts, S.4
De Moor, B.5
Rouzé, P.6
-
38
-
-
48449090922
-
RSAT: regulatory sequence analysis tools
-
Thomas-Chollier M., Sand O., Turatsinze J.V., Janky R., Defrance M., Vervisch E., et al. RSAT: regulatory sequence analysis tools. Nucleic Acids Res 2008, 36:W119-W127.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Thomas-Chollier, M.1
Sand, O.2
Turatsinze, J.V.3
Janky, R.4
Defrance, M.5
Vervisch, E.6
-
39
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
Tompa M., Li N., Bailey T.L., Church G.M., De Moor B., Eskin E., et al. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 2005, 23:137-144.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
De Moor, B.5
Eskin, E.6
-
40
-
-
4644292576
-
The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model
-
van Noort V., Snel B., Huynen M.A. The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep 2004, 5:280-284.
-
(2004)
EMBO Rep
, vol.5
, pp. 280-284
-
-
van Noort, V.1
Snel, B.2
Huynen, M.A.3
-
41
-
-
33644787637
-
Genome-wide identification of potential plant E2F target genes
-
Vandepoele K., Vlieghe K., Florquin K., Hennig L., Beemster G.T., Gruissem W., et al. Genome-wide identification of potential plant E2F target genes. Plant Physiol 2005, 139:316-328.
-
(2005)
Plant Physiol
, vol.139
, pp. 316-328
-
-
Vandepoele, K.1
Vlieghe, K.2
Florquin, K.3
Hennig, L.4
Beemster, G.T.5
Gruissem, W.6
-
42
-
-
66649122827
-
Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks
-
Vandepoele K., Quimbaya M., Casneuf T., De Veylder L., Peer Van de Y. Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol 2009, 150(2):535-546.
-
(2009)
Plant Physiol
, vol.150
, Issue.2
, pp. 535-546
-
-
Vandepoele, K.1
Quimbaya, M.2
Casneuf, T.3
De Veylder, L.4
Peer Van de, Y.5
-
43
-
-
77249100734
-
Network inference and network response identification: moving genome-scale data to the next level of biological discovery
-
Veiga D.F.T., Dutta B., Balázsi G. Network inference and network response identification: moving genome-scale data to the next level of biological discovery. Mol BioSyst 2010, 6:469-480.
-
(2010)
Mol BioSyst
, vol.6
, pp. 469-480
-
-
Veiga, D.F.T.1
Dutta, B.2
Balázsi, G.3
-
44
-
-
67949112687
-
Discovery of cis-elements between Sorghum and Rice using co-expression and evolutionary conservation
-
Wang X., Haberer G., Mayer K.F.X. Discovery of cis-elements between Sorghum and Rice using co-expression and evolutionary conservation. BMC Genomics 2009, 10:284.
-
(2009)
BMC Genomics
, vol.10
, pp. 284
-
-
Wang, X.1
Haberer, G.2
Mayer, K.F.X.3
-
45
-
-
0038631908
-
In silico identification of metazoan transcriptional regulatory regions
-
Wasserman W.W., Krivan W. In silico identification of metazoan transcriptional regulatory regions. Naturwissenschaften 2003, 90(4):156-166.
-
(2003)
Naturwissenschaften
, vol.90
, Issue.4
, pp. 156-166
-
-
Wasserman, W.W.1
Krivan, W.2
|